[gmx-users] ligand topology for opls.aa
Dear users i wanted to know if Acpyte generated topologies for a ligand are compatible with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa like ATP for gromos53a6.ff so that i can avoid manual approached like using gaussian . regards, Saman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 122, Issue 61
Dear Saman, You might want to consider OPLS-AA 2005 as implemented in the Shorodinger software. The Schrodinger Maestro is FREE for academia, after registering you can download it and use. There is an utility ffld_server, which is able to automatically assign OPLS-AA 2005 to any ligand molecule. Once you have the output of ffld_server, you can convert this into gromacs topology format by a python program called ffconv.py (see http://frolov-pchem.wikispaces.com/Downloads ). Also you can check if the conversion in your case was correct by check_conversion.sh script therein. This is well-documented and has real-life examples, so it is easy to start using this. See the documentation inside. Please give me your feedback if you use this tool. Kind regards, Andrey Fri, 13 Jun 2014 12:00:02 +0200 от gromacs.org_gmx-users-requ...@maillist.sys.kth.se: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. ligand topology for opls.aa (Saman Shahriyari) -- Message: 1 Date: Fri, 13 Jun 2014 01:32:46 -0700 (PDT) From: Saman Shahriyari samanshahriy...@yahoo.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: [gmx-users] ligand topology for opls.aa Message-ID: 1402648366.13559.yahoomail...@web163203.mail.gq1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear users i wanted to know if Acpyte generated topologies for a ligand are compatible with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa like ATP for gromos53a6.ff so that i can avoid manual approached like?using?gaussian . ?regards, Saman -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. End of gromacs.org_gmx-users Digest, Vol 122, Issue 61 ** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ligand topology for opls.aa
Пересылаемое сообщение От кого: Andrey Frolov andrey.i.fro...@mail.ru Кому: gromacs.org_gmx-users@maillist.sys.kth.se Копия: samanshahriy...@yahoo.com Дата: Fri, 13 Jun 2014 14:34:50 +0400 Тема: Re: gromacs.org_gmx-users Digest, Vol 122, Issue 61 Dear Saman, You might want to consider OPLS-AA 2005 as implemented in the Shorodinger software. The Schrodinger Maestro is FREE for academia, after registering you can download it and use. There is an utility ffld_server, which is able to automatically assign OPLS-AA 2005 to any ligand molecule. Once you have the output of ffld_server, you can convert this into gromacs topology format by a python program called ffconv.py (see http://frolov-pchem.wikispaces.com/Downloads ). Also you can check if the conversion in your case was correct by check_conversion.sh script therein. This is well-documented and has real-life examples, so it is easy to start using this. See the documentation inside. Please give me your feedback if you use this tool. Kind regards, Andrey Fri, 13 Jun 2014 12:00:02 +0200 от gromacs.org_gmx-users-requ...@maillist.sys.kth.se: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. ligand topology for opls.aa (Saman Shahriyari) -- Message: 1 Date: Fri, 13 Jun 2014 01:32:46 -0700 (PDT) From: Saman Shahriyari samanshahriy...@yahoo.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: [gmx-users] ligand topology for opls.aa Message-ID: 1402648366.13559.yahoomail...@web163203.mail.gq1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear users i wanted to know if Acpyte generated topologies for a ligand are compatible with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa like ATP for gromos53a6.ff so that i can avoid manual approached like?using?gaussian . ?regards, Saman -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. End of gromacs.org_gmx-users Digest, Vol 122, Issue 61 ** -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Adding polyatomic ions using genion or genbox ..
Dear Users: I would like to know if it is possible to add some polyatomic ions inside a pre-equilibrated (water + solute) system using genion or genbox...? I don't want to lose my equilibrated water around my macromolecule... If this is not possible can you give any piece of advice of how I can do it.. Thanks in advance -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] truncated octahedron box vector angles and number of waters
Dear All I am creating a truncated octahedron box and in vmd it appears as a rectangular box. In mailing list it has been suggested to use trjconv -ur compact option. But I have two issues, 1) I get box vector angle 70 90 70 with editconf and should be around 109 109 109 for a truncated octahedron box editconf -f input.gro -o output.gro -c -d 1.2 -bt octahedron system size : 12.324 14.348 5.952 (nm) diameter: 15.385 (nm) center : 7.774 7.569 7.829 (nm) box vectors : 12.324 14.348 5.952 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume :1052.41 (nm^3) shift : 1.119 5.007 -0.568 (nm) new center : 8.893 12.576 7.261 (nm) new box vectors : 17.785 17.785 17.785 (nm) new box angles : 70.53 109.47 70.53 (degrees) new box volume :4330.63 (nm^3) 2) I have a same system in AMBER and using truncated oct box with same 12 Angstrom water buffer but in Gromacs I get almost twice water molecules as I get in AMBER but with AMBER I get 109 109 109 vector angles. Just to add in AMBER I used the default value of closeness of solvent molecules being 1.0 Angs. I am not sure whats default in editconf (though I see it uses default water density value) Please suggest why I am getting different vector angles and number of waters? best regards JIom -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] truncated octahedron box vector angles and number of waters
Hi Jlom, The vectors depend on the orientation of the truncated octahedron, and on which three out of all possible vectors are chosen. As for the difference in water molecules, I don't know what AMBER does, but I can tell what Gromacs does. You have the diameter of the system, 15.385 nm, to which twice the 1.2 nm is added, giving the vector length 17.785 nm. A cube of that length would have a volume of 5625 nm^3, and a truncated octahedron is about 78% the volume of a cube, so it gives 0.78*(17.785**3) = 4388 nm^3. Well, there's some rounding..., the 4330.63 will be correct. Solvating that with genbox should give a pretty much correct amount of water. If AMBER gives you so much less, I'd guess there's something odd there. But, why not use a rhombic dodecahedron today? Cheers, Tsjerk On Fri, Jun 13, 2014 at 2:02 PM, gromacs query gromacsqu...@gmail.com wrote: Dear All I am creating a truncated octahedron box and in vmd it appears as a rectangular box. In mailing list it has been suggested to use trjconv -ur compact option. But I have two issues, 1) I get box vector angle 70 90 70 with editconf and should be around 109 109 109 for a truncated octahedron box editconf -f input.gro -o output.gro -c -d 1.2 -bt octahedron system size : 12.324 14.348 5.952 (nm) diameter: 15.385 (nm) center : 7.774 7.569 7.829 (nm) box vectors : 12.324 14.348 5.952 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume :1052.41 (nm^3) shift : 1.119 5.007 -0.568 (nm) new center : 8.893 12.576 7.261 (nm) new box vectors : 17.785 17.785 17.785 (nm) new box angles : 70.53 109.47 70.53 (degrees) new box volume :4330.63 (nm^3) 2) I have a same system in AMBER and using truncated oct box with same 12 Angstrom water buffer but in Gromacs I get almost twice water molecules as I get in AMBER but with AMBER I get 109 109 109 vector angles. Just to add in AMBER I used the default value of closeness of solvent molecules being 1.0 Angs. I am not sure whats default in editconf (though I see it uses default water density value) Please suggest why I am getting different vector angles and number of waters? best regards JIom -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Adding polyatomic ions using genion or genbox ..
On 6/13/14, 7:33 AM, Alberto Sergio Garay wrote: Dear Users: I would like to know if it is possible to add some polyatomic ions inside a pre-equilibrated (water + solute) system using genion or genbox...? I don't want to lose my equilibrated water around my macromolecule... If this is not possible can you give any piece of advice of how I can do it.. In either case (adding before or after solvation), genbox -ci -nmol is the way to go. Depending on the size of your polyatomic ions, they may fit in the pre-equilibrated system. If not, you could (in theory) strip the water from your existing system and save it to a coordinate file, then insert your polyatomic ions around the macromolecule, then re-solvate with the saved, equilibrated water. But if you're going to re-build it, re-equilibrating is trivial anyway, and probably less work. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes
On 6/13/14, 2:11 AM, sucharita dey wrote: Dear Users, I have a protein-DNA system with 3 Zinc fingers, 1 Fe++, 1 cofactor NOG (N-OxalyGlycine) and crystal waters. I have generated the initial topology of OGA from PRODRG and incorporated it in the the forcefield gromos 53a6 and since the forcefield already has parametrs for ZN and FE, I had no problem in generating the *.itp files. I solvated the system and ran steep minimization for 1000 steps with emstep = 0.1 and emtol 1. Is the NOG topology sound? PRODRG has known problems getting charges right, but building a suitable NOG topology from existing building blocks is trivial. It ran for ~80 steps and stopped. I checked the gro file generated, the problem is around OGA and the FE, and the OGA is loosing its structure. I suspect it due to clashes, -- actually in the crystal structure 2 oxygens of OGA are in co-ordination with the FE (the FE being co-ordinated with 4 other atoms including one O from crystal water). Sounds like a potential topology issue. One simple test is to run NOG in vacuo then in a box of water to see if it is stable on its own, then deal with it in the context of the full protein+ions. I have not considered the FE co-ordination, can you please suggest how to do this or else please suggest if you feel the problem is elsewhere. Ion coordination is easily done with distance restraints or type-6 harmonic connections. Below is the comment given after minimization stopped: *Energy minimization has stopped, but the forces havenot converged to therequested precision Fmax 1 (whichmay not be possible for your system). Itstoppedbecause the algorithm tried to make a new step whose sizewas toosmall, or there was no change in the energy sincelast step. Either way, weregard the minimization asconverged to within the available machineprecision,given your starting configuration and EM parameters.Double precision normally gives you higher accuracy, butthis is often notneeded for preparing to run moleculardynamics.writing lowest energy coordinates.Steepest Descents converged to machine precision in 84 steps,but did not reach the requested Fmax 1.Potential Energy = -3.7139549e+08Maximum force = 7.7602650e+14 on atom 4207Norm of force = 3.6179670e+12* NOTE: the atom 4207 with maximum force is FE You have essentially infinite forces, which indicate very bad geometry, clashes, or a bad topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] peculiar water behavior
On 6/12/14, 11:15 PM, Chetan Mahajan wrote: Dear All, I am simulating TiO2 crystal solvated by water and ions like sodium and formate. I am observing one peculiar thing, and I would like to rectify that. I have initial structure of crystal slab at the center of the box elongated in z-direction and almost equal boxlength on both the sides, with a gap of 1 nm between slab surface and first layer of water close to slab. This space is kept to avoid water going on the sides of the crystal during equilibration. This was a minor information. Now, the main observation is that during NPT equilibration, water from one side of the slab enters the other opposite side of the slab (using periodic conditions) so that boxlengths on both sides of the slab are very different at the end of equilibration. Is this an artifact of pressure coupling? Following is my equilibration .mdp file. I have tried varying the compressibility and tau-p parameters in the following file. e.g. zero compressibility in x/y direction or tau-p reduced to 3. With pressure coupling, any voids present in the system will be compressed. If you need to try to preserve some sort of vacuum layers, use NVT. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_clustsize
I can observe that GM1 molecules are separating from the DPPC molecules into GM1 domains. Is it possible to calculate the number of GM1 molecules in these GM1 domains? It worked with g_clustersize -cut 0.5 without the -mol option. I use the Martini force field. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_clustsize
Hi Raisa, I guess you know how many atoms are in a molecules, so you can divide the clustersize in atoms by it to get the number of molecules. Probably the biggest problem is that the output is in XPM format? I have a script (attached) to convert that to generic .dat format, which you can then process more naturally. Use as: ./xpm.py -f input.xpm -o output.dat Hope it helps, Tsjerk On Fri, Jun 13, 2014 at 2:55 PM, Raisa Kociurzynski rais...@gmx.net wrote: I can observe that GM1 molecules are separating from the DPPC molecules into GM1 domains. Is it possible to calculate the number of GM1 molecules in these GM1 domains? It worked with g_clustersize -cut 0.5 without the -mol option. I use the Martini force field. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] folding kinetics from SMD simulation
Dear All Is there any tool available to calculate folding kinetics form SMD simulation regards singam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS
Dear Prof. David van der Spoel, Thank you very much for considering g_mmpbsa for the GROMACS repository. We have a discussion on the same and will try to patch g_mmpbsa in the repository. Presently, we do not know how to integrate compilation procedure of g_mmpbsa with the GROMACS package as APBS libraries are required during compilation and Fortran compiler are required for the linking. Since I am travelling these days, hope we could able to work on the same in a month and so. With Regards Rashmi Kumari PhD Student School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi, India. On Tue, Jun 10, 2014 at 1:42 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2014-06-09 21:17, Rashmi wrote: Dear GROMACS users, We have developed a new tool, *g_mmpbsa* for GROMACS to carry out the MM-PBSA calculations. It uses APBS libraries for the Poisson-Boltzmann calculations. Features: - Include SASA, SAV and WCA -like non-polar models - It inherits threading (OpenMP) functions from APBS - Simultaneously calculate energy contribution s of residue s to binding Details of this tool are given in the following link: http://rashmikumari.github.io/g_mmpbsa/ Its implementation and testing are discussed in the following publication: http://pubs.acs.org/doi/abs/10.1021/ci500020m We would appreciate for suggestions regarding improvment of this tool. With Regards, Rashmi Kumari School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. Why not upload a patch to http://gerrit.gromacs.org ? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- With Regards, Rashmi Kumari Visting Student School of Chemistry and Molecular Biosciences (MD group) The University of Queensland St. Lucia, Brisbane, QLD 4072, Australia Contact No.- +61 434872368. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
Dr. Justin Lemkul, Now I understand the message about removal of bonds being just duplicate bonds that have been removed, and, also, I understand how the -ter flag works now. This is the screen output related to parsing of specbond.dat: 3 out of 3 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS1CYS1CYS5CYS5VAL6 CYS10 CYS10 N1 SG6 N47SG52 C59N101 SG106 CYS1 SG6 0.302 CYS5 N47 0.988 0.900 CYS5SG52 1.070 0.917 0.333 VAL6 C59 1.498 1.396 0.510 0.585 CYS10N101 1.122 0.901 0.614 0.609 0.835 CYS10 SG106 0.879 0.655 0.490 0.422 0.857 0.322 CYS15N160 0.784 0.488 1.066 0.984 1.477 0.774 0.620 CYS15 SG165 0.477 0.202 0.960 0.961 1.432 0.823 0.625 CYS17N184 1.030 0.784 0.721 0.460 1.004 0.617 0.387 CYS17 SG189 1.224 1.039 0.514 0.204 0.625 0.621 0.487 VAL21C245 0.756 0.685 0.408 0.388 0.847 0.812 0.531 CYS22N259 0.657 0.574 0.404 0.432 0.887 0.742 0.458 CYS22 SG264 0.755 0.588 0.371 0.430 0.827 0.436 0.203 VAL29C363 0.132 0.394 1.117 1.193 1.626 1.248 1.004 Here is precisely why your specbond.dat is not working - the bond criteria are not satisfied. The Cys1(N)-Val29(C) distance is 0.132 nm. You're specifing in specbond.dat (likely from simply copying the contents of the other lines) that the reference distance is 0.25 nm. If Gromacs does not find atoms within ±10% of the value in specbond.dat, a bond won't be created. Since 0.132 nm is way off, you won't get a bond. Also note that your final columns will try to rename the residues to CYS2 (which is specific for a disulfide cysteine, so unless that's true you'll get more fatal errors) and VAL2, which doesn't exist. See http://www.gromacs.org/Documentation/File_Formats/specbond.dat Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 -Matthew Stancea (This email chain has gotten a bit long in my opinion, so I have put the previous email below. With your permission, I would prefer just using the above message in order to continue correspondence in shorter emails; however, if you would prefer to instead use the entire email, I completely understand.) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, June 12, 2014 5:01 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Using specbond.dat in pdb2gmx On 6/12/14, 4:53 PM, Matthew Stancea wrote: On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the option -ignh at the end of my command, but doing so deletes the bond between the first nitrogen and the last carbon (which should be connected for this peptide to be cyclic) and adds two additional hydrogens and a positive charge to the first nitrogen and an additional oxygen and a negative charge to the last carbon, rendering this peptide as non-cyclic. After searching around for quite a while, I found out that many others on this mailing list were having the same issues as myself, and some replies to their messages including the usage of a file known as specbond.dat which may be helpful in retaining that bond. The -ignh flag is not relevant to those observations. In my working directory, I have a file named specbond.dat and it contains the following information: 3 CYS N 1 VAL C 1 0.25CYS2VAL2 CYS SG 1 CYS SG 1 0.25CYS2CYS2 CYM SG 1 CYM SG 1 0.25CYS2CYS2 When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp while specbond.dat is in the working directory (Here is a link for the structure of peptide 1NB1 for reference if needed: http://www.ncbi.nlm.nih.gov/protein/1NB1_A ), I get the following message: --- Program pdb2gmx_mpi,
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/13/14, 12:57 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Now I understand the message about removal of bonds being just duplicate bonds that have been removed, and, also, I understand how the -ter flag works now. This is the screen output related to parsing of specbond.dat: 3 out of 3 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS1CYS1CYS5CYS5VAL6 CYS10 CYS10 N1 SG6 N47SG52 C59N101 SG106 CYS1 SG6 0.302 CYS5 N47 0.988 0.900 CYS5SG52 1.070 0.917 0.333 VAL6 C59 1.498 1.396 0.510 0.585 CYS10N101 1.122 0.901 0.614 0.609 0.835 CYS10 SG106 0.879 0.655 0.490 0.422 0.857 0.322 CYS15N160 0.784 0.488 1.066 0.984 1.477 0.774 0.620 CYS15 SG165 0.477 0.202 0.960 0.961 1.432 0.823 0.625 CYS17N184 1.030 0.784 0.721 0.460 1.004 0.617 0.387 CYS17 SG189 1.224 1.039 0.514 0.204 0.625 0.621 0.487 VAL21C245 0.756 0.685 0.408 0.388 0.847 0.812 0.531 CYS22N259 0.657 0.574 0.404 0.432 0.887 0.742 0.458 CYS22 SG264 0.755 0.588 0.371 0.430 0.827 0.436 0.203 VAL29C363 0.132 0.394 1.117 1.193 1.626 1.248 1.004 Here is precisely why your specbond.dat is not working - the bond criteria are not satisfied. The Cys1(N)-Val29(C) distance is 0.132 nm. You're specifing in specbond.dat (likely from simply copying the contents of the other lines) that the reference distance is 0.25 nm. If Gromacs does not find atoms within ±10% of the value in specbond.dat, a bond won't be created. Since 0.132 nm is way off, you won't get a bond. Also note that your final columns will try to rename the residues to CYS2 (which is specific for a disulfide cysteine, so unless that's true you'll get more fatal errors) and VAL2, which doesn't exist. See http://www.gromacs.org/Documentation/File_Formats/specbond.dat Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 -Matthew Stancea (This email chain has gotten a bit long in my opinion, so I have put the previous email below. With your permission, I would prefer just using the above message in order to continue correspondence in shorter emails; however, if you would prefer to instead use the entire email, I completely understand.) Snipping out relevant portions is perfectly fine (and preferred) as long as you don't nuke something actually important. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] peculiar water behavior
Hi Justin, I, actually, do not want to preserve any voids. Initial void that I mentioned is supposed to be filled by water during equilibration and it does so. However, problem is that some or major quantity of water moves out from one side of the box to enter from the opposite side (obeying periodic boundary conditions) and crystal slab moving following water movement. Thus although initially there is almost equal amount of water on both sides of the slab, we have more water on one side of the slab than the other side after equilibration. In other words, length of the box on one side of the slab is more than the other side after equilibration, although it is same on both sides before equilibration. My dilemma is whether this is due to pressure coupling or any gromacs thing or due to potentials (mixed buckingham and LJ)? Thanks Chetan On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/14, 11:15 PM, Chetan Mahajan wrote: Dear All, I am simulating TiO2 crystal solvated by water and ions like sodium and formate. I am observing one peculiar thing, and I would like to rectify that. I have initial structure of crystal slab at the center of the box elongated in z-direction and almost equal boxlength on both the sides, with a gap of 1 nm between slab surface and first layer of water close to slab. This space is kept to avoid water going on the sides of the crystal during equilibration. This was a minor information. Now, the main observation is that during NPT equilibration, water from one side of the slab enters the other opposite side of the slab (using periodic conditions) so that boxlengths on both sides of the slab are very different at the end of equilibration. Is this an artifact of pressure coupling? Following is my equilibration .mdp file. I have tried varying the compressibility and tau-p parameters in the following file. e.g. zero compressibility in x/y direction or tau-p reduced to 3. With pressure coupling, any voids present in the system will be compressed. If you need to try to preserve some sort of vacuum layers, use NVT. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] New Molecule Topology
Hi, I've got very pleasant answer from ATB. They provided me with a link for manually optimized topology of cholesterol (GROMOS53A6): http://compbio.biosci.uq.edu.au/atb/molecule.py?molid=1731 and I have found manually optimized POPC topology (GROMOS54A7) : http://compbio.biosci.uq.edu.au/atb/molecule.py?molid=1506 Now I have two question: 1. May I combine cholesterol G53A6 topology with POPC taken from Prof. Tieleman's webpage in order to get cholesteryl oleate topology? 2. What about combining cholesterol G53A6 with POPC G54A7 for the same purpose? Thank you! On Tue, Jun 3, 2014 at 5:47 PM, Todor Antonijevic t_ant...@uncg.edu wrote: Hi, I tried ATB but it has wrong database files. For example, Gromacs united atom .itp file is missing Carbon 28,29 and 30. I hope I will get help from them on this matter. Thank you On Fri, May 30, 2014 at 2:06 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: I think the Ausi ATB is a bit beter for initial topologies,but still needs some input afterwards. They usually have less to change around needed, or beter charge sets, but tend to have problems with adding a hydrogen. Only for 53a6 though. Also, just loking at the ff topoloy you canput one together from scratch from what is already in gromacs, but painfull...there are a large amunt of MD's with all atom or berger lipids in a 53a6 which should work with a7 as well, and the ATB has a few constructed all or UA lipids, cholestorols on its site already done... My opinion, Stephan Watkins *Gesendet:* Donnerstag, 29. Mai 2014 um 16:55 Uhr *Von:* Todor Antonijevic t_ant...@uncg.edu *An:* gmx-us...@gromacs.org *Betreff:* Re: [gmx-users] New Molecule Topology Hi Justin, Thank you for you answer. It sounds to me that using PRODRG server for the initial topology and then correcting atom types and other parameters according to Berger lipids is acceptable method. What about constructing cholesteryl oleate molecule by gluing together known cholesterol force field with oleate chain taken from POPC? Thank you in advance, Anton On Wed, May 28, 2014 at 8:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/28/14, 1:33 PM, Todor Antonijevic wrote: Hi, I would like to create a topology file for cholesteryl oleate molecule. Is it a good practice to use PRODRG server to generate all connections, and then to change atom types and parameters according to the Berger force field? Is there a better approach? No matter how you produce the initial topology (PRODRG, ATB, etc), you'll likely end up gutting nearly the entire topology to replace the atom types, charges, and bonded parameters. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -inf potential with TPIC
Hi João, I dont think its an excessive number of unfavorable insertions. The mu getting output with double precision are Reading frame 40 time 1770.000 mu -6.570e+01 mu -7.654e+01 Reading frame 50 time 1775.000 mu -4.985e+01 mu -7.609e+01 Reading frame 60 time 1780.000 mu -7.010e+01 mu -7.571e+01 Reading frame 70 time 1785.000 mu -5.669e+01 mu -7.540e+01 Reading frame 80 time 1790.000 mu -4.749e+01 mu -7.511e+01 Reading frame 90 time 1795.000 mu -7.355e+01 mu -7.590e+01 to give a fairly representative sample. So, no, they arent near 100, and are negative... And the issue seems to happen with later insertions, not the first few... One run I just did, only the very last average mu was -inf, (not even the mu for that frame, just the average mu after that frame) which really seems to imply some sort of overflow problem Reading frame 180 time 1790.000 mu -1.284e+02 mu -1.153e+02 Reading frame 190 time 1795.000 mu -7.920e+01 mu -inf (not the same run as above, this was run in single precision) On Thu, Jun 12, 2014 at 7:06 AM, João M. Damas jmda...@itqb.unl.pt wrote: Hello Rafael, High energies (energy differences) are not discarded. When summing them through the exponential of their negative, they contribute very little to the final sum (lower energies dominate the sum). Hence, they are discarded. The -inf value on the mu standard error output is normal because, unlike the -tpi output, there is no ternary operator checking if the sum of exponentials is equal to zero (when it is, the log of zero gives you the inf value). The change to the double precision not giving you the -inf also makes sense, because the sum of exponentials, which on single-precision was zero, can now be non-zero due to the higher number of decimal places on double-precision. I am guessing with double-precision you are getting very high positive numbers (energies) for the mu, around 1000 maybe? My interpretation is that it is hard to find a favorable place to insert the water molecule in that cavity, at least with a few frames. I am guessing that with more and more frames, that may change, which is natural. I hope this has helped. Cheers, João On Thu, Jun 12, 2014 at 10:45 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/14, 8:55 PM, Rafael I. Silverman y de la Vega wrote: I mistyped amber, when I should have typed charmm, amber is totally uninvolved in my calculations. I used the script from http://www.gromacs.org/Downloads/User_contributions/Other_software titled charmm2gromacs. The output looked fine after running it. And, I doubt its the cofactor, just ran the insertion with double precision mdrun, it gave reasonable looking results. There seems to be some sort of issue with unreasonable interaction energies not being discarded properly. It's entirely possible that there's something wrong with the tpic code; you can certainly file a bug report on Redmine with input files to reproduce it. -Justin On Tue, Jun 10, 2014 at 3:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 6:14 PM, Rafael I. Silverman y de la Vega wrote: I meant that I only changed to cofactor to gromacs chamm27 format, not amber format. I used charmm27 for the apoprotein as well as the cofactor. What script did you use? I don't understand why Amber99SB is involved here, so I don't know exactly what you were doing to create the topology. It may not end up being useful information, but it's important to establish the validity of the underlying physical model. -Justin On Tue, Jun 10, 2014 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 6:04 PM, Rafael I. Silverman y de la Vega wrote: you think it was the cofactor model? If you're using a CHARMM-parametrized cofactor with an Amber99SB protein, I'd say the simulations are wholly unreliable. It's certainly the #1 likely cause for nonsensical results. If you want to get to the root of the issue, you need to start with a solid foundation. Unless that's not what your last message meant? When you say only changed the cofactor, that implied to me that you didn't consistently convert everything in the system. -Justin On Tue, Jun 10, 2014 at 2:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 5:01 PM, Rafael I. Silverman y de la Vega wrote: wait, I only changed the cofactor to gromacs charmm27.ff format Pretty amazing that the simulation even ran with that mash-up of parameters :) I'd say that's the most likely cause of your problems; nonsensical physical model leads to nonsensical output. -Justin On Tue, Jun 10, 2014 at 1:58 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: I suppose something might be wrong with the simulations. I am using gromacs 4.6.5, I am
[gmx-users] How to rotate box in editconf
Dear gmx-users, Sorry, for asking such a simple question. But I didn't get any satisfactory answer searching through mailing lists. I have prepared a mixed bilayer system containing 300 lipids with box size 10 10 14 (nm). Visualization confirmed that bilayer is formed in X-Y plane. But, in order to see bilayer edge along z-axis, I need to exchange my x and z coodinates of this bilayer system. For this, I use editconf utility as: editconf -f bilayer.gro -rotate -90 -90 -90 -o newbox.gro However, as expected editconf only rotates molecule coordinates in desired direction but simulation box remain unchanged. I tried building a new box using editconf (suggested by some mailing posts) around it but still my problem is not solved. editconf -f newbox.gro -box 10 10 14 -o rotate-box.gro Can anyone please let me know how to shift simulation box around this shifted system. Thanks, Rini -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] peculiar water behavior
Other main observation is that crystal slab following water, moving in the same direction, *despite of position restraints (refcoord-scaling=com option). * Thanks Chetan On Fri, Jun 13, 2014 at 1:45 PM, Chetan Mahajan chetanv...@gmail.com wrote: Hi Justin, I, actually, do not want to preserve any voids. Initial void that I mentioned is supposed to be filled by water during equilibration and it does so. However, problem is that some or major quantity of water moves out from one side of the box to enter from the opposite side (obeying periodic boundary conditions) and crystal slab moving following water movement. Thus although initially there is almost equal amount of water on both sides of the slab, we have more water on one side of the slab than the other side after equilibration. In other words, length of the box on one side of the slab is more than the other side after equilibration, although it is same on both sides before equilibration. My dilemma is whether this is due to pressure coupling or any gromacs thing or due to potentials (mixed buckingham and LJ)? Thanks Chetan On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/14, 11:15 PM, Chetan Mahajan wrote: Dear All, I am simulating TiO2 crystal solvated by water and ions like sodium and formate. I am observing one peculiar thing, and I would like to rectify that. I have initial structure of crystal slab at the center of the box elongated in z-direction and almost equal boxlength on both the sides, with a gap of 1 nm between slab surface and first layer of water close to slab. This space is kept to avoid water going on the sides of the crystal during equilibration. This was a minor information. Now, the main observation is that during NPT equilibration, water from one side of the slab enters the other opposite side of the slab (using periodic conditions) so that boxlengths on both sides of the slab are very different at the end of equilibration. Is this an artifact of pressure coupling? Following is my equilibration .mdp file. I have tried varying the compressibility and tau-p parameters in the following file. e.g. zero compressibility in x/y direction or tau-p reduced to 3. With pressure coupling, any voids present in the system will be compressed. If you need to try to preserve some sort of vacuum layers, use NVT. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -inf potential with TPIC
Interesting... Does it also happen on the mu or only on the mu? I ask this because the mu, unlike the mu, has the volume in it (as per the Widom insertion equations for the isothermic-isobaric ensemble). If the -inf is only on the mu, I'd suggest checking the volume along the trajectory (using g_energy, for example, or check the .xvg file from the -tpi flag, which already has the volume, I think). Check the post-processed trajectory that you feed mdrun -rerun, as your trajectory-processing script for TPIC may be doing something strange to the box size. I recognize that the single/double-precision is intriguing, if indeed the problem is the volume. João On Fri, Jun 13, 2014 at 11:10 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: Hi João, I dont think its an excessive number of unfavorable insertions. The mu getting output with double precision are Reading frame 40 time 1770.000 mu -6.570e+01 mu -7.654e+01 Reading frame 50 time 1775.000 mu -4.985e+01 mu -7.609e+01 Reading frame 60 time 1780.000 mu -7.010e+01 mu -7.571e+01 Reading frame 70 time 1785.000 mu -5.669e+01 mu -7.540e+01 Reading frame 80 time 1790.000 mu -4.749e+01 mu -7.511e+01 Reading frame 90 time 1795.000 mu -7.355e+01 mu -7.590e+01 to give a fairly representative sample. So, no, they arent near 100, and are negative... And the issue seems to happen with later insertions, not the first few... One run I just did, only the very last average mu was -inf, (not even the mu for that frame, just the average mu after that frame) which really seems to imply some sort of overflow problem Reading frame 180 time 1790.000 mu -1.284e+02 mu -1.153e+02 Reading frame 190 time 1795.000 mu -7.920e+01 mu -inf (not the same run as above, this was run in single precision) On Thu, Jun 12, 2014 at 7:06 AM, João M. Damas jmda...@itqb.unl.pt wrote: Hello Rafael, High energies (energy differences) are not discarded. When summing them through the exponential of their negative, they contribute very little to the final sum (lower energies dominate the sum). Hence, they are discarded. The -inf value on the mu standard error output is normal because, unlike the -tpi output, there is no ternary operator checking if the sum of exponentials is equal to zero (when it is, the log of zero gives you the inf value). The change to the double precision not giving you the -inf also makes sense, because the sum of exponentials, which on single-precision was zero, can now be non-zero due to the higher number of decimal places on double-precision. I am guessing with double-precision you are getting very high positive numbers (energies) for the mu, around 1000 maybe? My interpretation is that it is hard to find a favorable place to insert the water molecule in that cavity, at least with a few frames. I am guessing that with more and more frames, that may change, which is natural. I hope this has helped. Cheers, João On Thu, Jun 12, 2014 at 10:45 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/14, 8:55 PM, Rafael I. Silverman y de la Vega wrote: I mistyped amber, when I should have typed charmm, amber is totally uninvolved in my calculations. I used the script from http://www.gromacs.org/Downloads/User_contributions/Other_software titled charmm2gromacs. The output looked fine after running it. And, I doubt its the cofactor, just ran the insertion with double precision mdrun, it gave reasonable looking results. There seems to be some sort of issue with unreasonable interaction energies not being discarded properly. It's entirely possible that there's something wrong with the tpic code; you can certainly file a bug report on Redmine with input files to reproduce it. -Justin On Tue, Jun 10, 2014 at 3:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 6:14 PM, Rafael I. Silverman y de la Vega wrote: I meant that I only changed to cofactor to gromacs chamm27 format, not amber format. I used charmm27 for the apoprotein as well as the cofactor. What script did you use? I don't understand why Amber99SB is involved here, so I don't know exactly what you were doing to create the topology. It may not end up being useful information, but it's important to establish the validity of the underlying physical model. -Justin On Tue, Jun 10, 2014 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 6:04 PM, Rafael I. Silverman y de la Vega wrote: you think it was the cofactor model? If you're using a CHARMM-parametrized cofactor with an Amber99SB protein, I'd say the simulations are wholly unreliable. It's certainly the #1 likely cause for nonsensical results. If you want to get to the root of the issue, you need to start
